Genomic relationships among Nicotiana species with different ploidy levels revealed by 5S rDNA spacer sequences and FISH/GISH

Kitamura, Satoshi; Tanaka, Atsushi; Inoue, Masayoshi

doi:10.1266/ggs.80.251

Cited by 13 publications

(12 citation statements)

References 36 publications

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“…Genomic in situ hybridization (GISH) provides a visual and direct method for investigating genomic composition among species, and is especially useful in elucidating the complex origins of polyploid plants. This technique has been already applied in many groups such as Triticeae [25], Brassica [26], Nicotiana [27], Andropogon [28], and Setaria species [19,20]. In this report, GISH was applied to chromosome preparations of Setaria species of Eurasian origin with unknown genome constitution.…”

Section: Introductionmentioning

confidence: 99%

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Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

et al. 2013

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BackgroundThe Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide.ResultsGISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus.ConclusionsThree novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC’C’. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

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Section: Introductionmentioning

confidence: 99%

“…To further confirm the results obtained by GISH, 5S rDNA and knotted1 gene sequences were analyzed using Bayesian methods to elucidate their phylogenetic relationships. Sequences of 5S rDNA and knotted1 genes have already useful in the phylogenetic study of many plant species and of Setaria relationship in particular [9,14,27]. …”

Section: Introductionmentioning

confidence: 99%

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

et al. 2013

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“…Noctiflorae in the origin of sect. Suaveolentes species were also inferred by Kitamura et al (2005) on the basis of GISH and 5S nrDNA sequence data, with N. glauca (sect. Noctiflorae ) identified as a putative parent of one sect.…”

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confidence: 99%

“…Therefore, the conclusions regarding the origin of sect. Suaveolentes drawn by Kitamura et al (2005) might change given a more comprehensive sampling of taxa and 5S sequence variation. A more recent study using a region of the low‐copy nuclear gene nuclear‐encoded plastid‐expressed GLUTAMINE SYNTHETASE ( GS ), which has retained both parental copy types (unlike ITS), placed one homoeolog with the diploid N. sylvestris (the sole member of sect.…”

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confidence: 99%

RECONSTRUCTING THE COMPLEX EVOLUTIONARY ORIGIN OF WILD ALLOPOLYPLOID TOBACCOS (NICOTIANASECTIONSUAVEOLENTES)

et al. 2012

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Nicotiana (Solanaceae) provides an ideal system for understanding polyploidization, a pervasive and powerful evolutionary force in plants, as this genus contains several groups of allotetraploids that formed at different times from different diploid progenitors.However, the parental lineages of the largest group of allotetraploids, Nicotiana section Suaveolentes, have been problematic to identify. Using data from four regions of three low-copy nuclear genes, nuclear ribosomal DNA, and regions of the plastid genome, we have reconstructed the evolutionary origin of sect. Suaveolentes and identified the most likely diploid progenitors by using a combination of gene trees and network approaches to uncover the most strongly supported evidence of species relationships. Our analyses best support a scenario where a member of the sect. Sylvestres lineage acted as the paternal progenitor and a member of either sect. Petunioides or sect. Noctiflorae that also contained introgressed DNA from the other, or a hypothetical hybrid species between these two sections, was the maternal progenitor. Nicotiana exemplifies many of the factors that can complicate the reconstruction of polyploid evolutionary history and highlights how reticulate evolution at the diploid level can add even greater complexity to allopolyploid genomes.

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“…Our method was successfully used to prepare meiotic chromosomes from a Nicotiana plant, cabbage, and maize. Nicotiana plants have been usually used for allotetraplod evolutionary research and classification studies based on cytogenetic analyses [ 24 – 26 ]. Cabbage is a plant in Brassica , which is very important for vegetable and oil production.…”

Section: Discussionmentioning

confidence: 99%

A modified method for preparing meiotic chromosomes based on digesting pollen mother cells in suspension

et al. 2015

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BackgroundMeiotic chromosome preparation is a key step in plant meiotic research. Pollen mother cell (PMC) wall elimination is beneficial to cytogenetic experimental procedures. Without wall interference, these procedures are easier and more successful. In existing methods it is difficult to eliminate PMC walls completely and uniformly. In this paper, we present an improved method for digesting PMC walls, and one for providing massive chromosomal spreads on a slide for other cytogenetic experimental procedures.ResultsThree plants were selected to exhibit the modified meiotic chromosome preparation method. PMCs were dispersed as single cells and incubated in a mixed enzyme solution (3 % cellulose + 0.3 % pectinase + 1 % snailase) for 1.5–2.5 h. In total, 28.28 % cells were lost during this process. There were 800–1900 spreads on every slide and no PMC wall interference was found on any of the slides. The spreads were also evenly distributed on the slides. More spreads were obtained when PMC and protoplast densities in the suspension were increased. All three plants’ spreads were successfully used to locate a 5 s rDNA conserved sequence. The Nicotiana hybrid’s spreads were successfully used to identify the hybrid’s parental genome.ConclusionThis is an alternative method for meiotic chromosome preparation. Through this method, PMC walls can be completely and uniformly eliminated, and hundreds of spreads on every slide can be obtained. These spreads can be successfully used for DNA in situ hybridization.

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Genomic relationships among Nicotiana species with different ploidy levels revealed by 5S rDNA spacer sequences and FISH/GISH

Cited by 13 publications

References 36 publications

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

RECONSTRUCTING THE COMPLEX EVOLUTIONARY ORIGIN OF WILD ALLOPOLYPLOID TOBACCOS (NICOTIANASECTIONSUAVEOLENTES)

A modified method for preparing meiotic chromosomes based on digesting pollen mother cells in suspension

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